5UDI

IFIT1 monomeric mutant (L457E/L464E) with m7Gppp-AAAA (syn and anti conformations of cap)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations.

Abbas, Y.M.Laudenbach, B.T.Martinez-Montero, S.Cencic, R.Habjan, M.Pichlmair, A.Damha, M.J.Pelletier, J.Nagar, B.

(2017) Proc Natl Acad Sci U S A 114: E2106-E2115

  • DOI: 10.1073/pnas.1612444114
  • Primary Citation of Related Structures:  
    5UDL, 5UDI, 5UDK, 5UDJ

  • PubMed Abstract: 
  • IFIT1 (IFN-induced protein with tetratricopeptide repeats-1) is an effector of the host innate immune antiviral response that prevents propagation of virus infection by selectively inhibiting translation of viral mRNA. It relies on its ability to com ...

    IFIT1 (IFN-induced protein with tetratricopeptide repeats-1) is an effector of the host innate immune antiviral response that prevents propagation of virus infection by selectively inhibiting translation of viral mRNA. It relies on its ability to compete with the translation initiation factor eIF4F to specifically recognize foreign capped mRNAs, while remaining inactive against host mRNAs marked by ribose 2'-O methylation at the first cap-proximal nucleotide (N1). We report here several crystal structures of RNA-bound human IFIT1, including a 1.6-Å complex with capped RNA. IFIT1 forms a water-filled, positively charged RNA-binding tunnel with a separate hydrophobic extension that unexpectedly engages the cap in multiple conformations ( syn and anti ) giving rise to a relatively plastic and nonspecific mode of binding, in stark contrast to eIF4E. Cap-proximal nucleotides encircled by the tunnel provide affinity to compete with eIF4F while allowing IFIT1 to select against N1 methylated mRNA. Gel-shift binding assays confirm that N1 methylation interferes with IFIT1 binding, but in an RNA-dependent manner, whereas translation assays reveal that N1 methylation alone is not sufficient to prevent mRNA recognition at high IFIT1 concentrations. Structural and functional analysis show that 2'-O methylation at N2, another abundant mRNA modification, is also detrimental for RNA binding, thus revealing a potentially synergistic role for it in self- versus nonself-mRNA discernment. Finally, structure-guided mutational analysis confirms the importance of RNA binding for IFIT1 restriction of a human coronavirus mutant lacking viral N1 methylation. Our structural and biochemical analysis sheds new light on the molecular basis for IFIT1 translational inhibition of capped viral RNA.


    Organizational Affiliation

    Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, QC, Canada H3G 0B1; bhushan.nagar@mcgill.ca.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced protein with tetratricopeptide repeats 1A479Homo sapiensMutation(s): 2 
Gene Names: IFIT1G10P1IFI56IFNAI1ISG56
Find proteins for P09914 (Homo sapiens)
Explore P09914 
Go to UniProtKB:  P09914
NIH Common Fund Data Resources
PHAROS  P09914
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*(GTA))-R(P*AP*AP*A)-3')B4unidentified
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PGE
    Query on PGE

    Download CCD File 
    A
    TRIETHYLENE GLYCOL
    C6 H14 O4
    ZIBGPFATKBEMQZ-UHFFFAOYSA-N
     Ligand Interaction
    CA
    Query on CA

    Download CCD File 
    A
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.58 Å
    • R-Value Free: 0.178 
    • R-Value Work: 0.157 
    • R-Value Observed: 0.158 
    • Space Group: P 42 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 111.715α = 90
    b = 111.715β = 90
    c = 93.157γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data scaling
    PDB_EXTRACTdata extraction
    Cootmodel building
    PHASERphasing
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Canadian Institutes of Health Research (CIHR)CanadaMOP-133535

    Revision History 

    • Version 1.0: 2017-03-01
      Type: Initial release
    • Version 1.1: 2017-03-15
      Changes: Database references
    • Version 1.2: 2017-03-22
      Changes: Database references
    • Version 1.3: 2017-11-22
      Changes: Refinement description
    • Version 1.4: 2020-01-08
      Changes: Author supporting evidence, Database references